crux create-index

Usage:

crux create-index [options] <protein input file> <index name>

Description:

Given a protein fasta sequence database as input, generate an index of all of its peptides and save it to disk. This index can be used with crux-search-for-matches instead of the fasta file to speed up the search.

Input:

• <protein input file> – The name of the file (in fasta format) from which to parse proteins.
• <index name> – The name of the directory where the newly created index will be placed.

Output:

The main output of the program is an index for the fasta file. An index consists of a directory containing three types of files: binary index files, binary sequence files, and a text file with settings. The directory is named <index name>. The binary sequence file will be named after the input file and ending with 'binary_fasta'. The text file is named README. Nothing is printed to STDOUT. Diagnostic messages are printed to STDERR depending on the level of verbosity. (see options below)

Options:

• --min-mass <float> – The minimum neutral mass of the peptides to place in the index. Default = 200.
• --max-mass <float> – The maximum neutral mass of the peptides to place in index. Default = 7200.
• --min-length <int> – The minimum length of the peptides to place in the index. Default = 6.
• --max-length <int> – The maximum length of the peptides to place in the index. Default = 50.
• enzyme <trypsin|chymotrypsin|elastase|clostripain|cyanogen-bromide|idosobenzoate|proline-endopeptidase|staph-protease|modified-chymotrypsin|elastase-trypsin-chymotrypsin|no-enzyme> – Enzyme to use for in silico digestion of protein sequences. Used in conjunction with the options digestion and missed-cleavages. Use 'no-enzyme' for non-specific digestion. Digestion rules are as follows: enzyme name [cuts after one of these residues]|{but not before one of these residues}. trypsin [RK]|{P}, elastase [ALIV]|{P}, chymotrypsin [FWY]|{P}, clostripain [R]|[], cyanogen-bromide [M]|[], iodosobenzoate [W]|[], proline-endopeptidase [P]|[], staph-protease [E]|[], modified-chymotrypsin [FWYL]|{P}, elastase-trypsin-chymotrypsin [ALIVKRWFY]|{P},aspn []|[D] (cuts before D). Default = trypsin.
• custom-enzyme <residues before cleavage | residues after cleavage > &ndash Specify rules for in silico digestion of protein sequences. Overrides the enzyme option. Two lists of residues are given enclosed in square brackets or curly braces and separated by a |. The first list contains residues required/prohibited before the cleavage site and the second list is residues after the cleavage site. If the residues are required for digestion, they are in square brackets, '[' and ']'. If the residues prevent digestion, then they are enclosed in curly braces, '{' and '}'. Use X to indicate all residues. For example, trypsin cuts after R or K but not before P which is represented as [RK]|{P}. AspN cuts after any residue but only before D which is represented as [X]|[D].
• --digestion <full-digest|partial-digest> Degree of digestion used to generate peptides (full-digest, partial-digest). Either both ends or one end of a peptide must conform to enzyme specificity rules. Default full-digest., Used in conjunction with enzyme option when enzyme is not set to to 'no-enzyme'.
• --missed-cleavages <T|F> – Allow missed cleavage sites within a peptide. When used with enzyme specified includes peptides containing one or more potential cleavage sites. Default = F.
• --isotopic-mass <average|mono> – Specify the type of isotopic masses to use when calculating the peptide mass. Default = average.
• --overwrite <T|F> Replace existing files if true (T) or fail when trying to overwrite a file if false (F). Default = F.
• --parameter-file <string> A file containing command-line or additional parameters. See the parameter documentation page for details.
• --verbosity <0-100> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = 30.
• --version T – Print the version number and quit. Please note that you must include the 'T' after --version.

Parameter file options:

• <A-Z> <float> – Specify static modifications. This is a mass change applied to the given amino acid (in single-letter-code A thru Z) for every peptide in which it occurs. Use the mod option for generating peptides both with and without the mass change. Default C=57.

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